Tailor

Tailor is a Burrows–Wheeler transform (BWT) based fast aligner specialized in discovering non-templated addition of nucleotide to the 3' end of nucleic acids (a.k.a., tailing) from Next Generation Sequencing data.

Tailor is released under GPLv2 with additional restriction so that is only applicable to individuals and non-profits and that any for-profit company must purchase a different license.

A Shell based pipelines are provided using fastq as input and produce publication quality figures.

INSTALL

*Only 64 bits systems are able to compile and run Tailor.

Run the binary directly without installation

Please try the precompiled binaries first, most of the linux systems should be able to run Tailor without any troubles.

bin/tailor_linux        # for linux
bin/tailor_mac_x64      # for OSX

Or you can find them in the release tab in this page or at this link.

Compile from the source code

Install the dependencies

1.1 Relative recent C++ compiler that support most features of C++11. We recommend GCC.
1.2 Boost
1.3 CMake

Get the latest version of the software

git clone git@github.com:jhhung/Tailor.git

Enter the folder Tailor and:

Set environmental variable $BOOST_ROOT to the directory of boost if CMake cannot find boost automatically;
Set environmental variable $CC and $CXX to the gcc/g++ compiler you want to use.

cmake .

Compile the software by typing:

make

troubleshooting

If you got linker error, it is possible that the default library in the lib/ is not suitable to your platform. There are two libraries available, one is for Mac OSX one is for Linux, rename the one that fit the best to "libabwt_table.a", and retype

make

USAGE

tailor

Build genomic index (similar to bowtie-build)

tailor build -i genome.fa -p genome

Mapping

tailor map -p genome -n 8 -i smallRNA.fq

tailing pipeline

# reads.fq: input reads in fastq format: 
# dm3.fa: genome sequence in fasta format; it will generate index in the index folder of tailor directory, if it doesn't exist
# genomic_feature_file; used to generate figures for different genomic features (exon, intron...). See our example in the annotation folder to make such file
# using 24 CPUs
# use PHRED score 20 as filter: only reads with every base equal to to higher than 20 pass the filter and enters the pipeline
run_miRNA_tailing_pipeline.sh \ 
    -i reads.fq  \ 
    -g dm3.fa \ 
    -t genomic_feature_file \ 
    -o output_dir \ 
    -c 24 \ 
    -q 20

Download

Indexes

Tailor indexes

# You can find all the pre-bulit indexes in:
http://www.jhhlab.tw/Tailor/index/

# Human:
http://www.jhhlab.tw/Tailor/index/hg18.tar.gz
http://www.jhhlab.tw/Tailor/index/hg19.tar.gz

# Mouse:
http://www.jhhlab.tw/Tailor/index/mm9.tar.gz
http://www.jhhlab.tw/Tailor/index/mm10.tar.gz

# for downloading
lftp -c "pget -n 4 http://www.jhhlab.tw/Tailor/index/hg18.tar.gz"

Speed test files for the publication

You can download all the related files for the speed test from the link

http://www.jhhlab.tw/Tailor/speed_test_samples/

And the links of original data for non-tailed and tailed reads

http://www.jhhlab.tw/Tailor/speed_test_samples/Drosophila_melanogaster.2m.fq
http://www.jhhlab.tw/Tailor/speed_test_samples/Drosophila_melanogaster.all.randomeTailed.fq

And the speed test log (3 times)

http://www.jhhlab.tw/Tailor/speed_test_samples/test_speed.log
http://www.jhhlab.tw/Tailor/speed_test_samples/test_speed.log2
http://www.jhhlab.tw/Tailor/speed_test_samples/test_speed.log3

And the speed log for bowtie tailing

http://www.jhhlab.tw/Tailor/speed_test_samples/tailing.log
http://www.jhhlab.tw/Tailor/speed_test_samples/tailing.log2
http://www.jhhlab.tw/Tailor/speed_test_samples/tailing.log3

All scripts for speed test can be found in the utils directory

Citing Tailor

Chou, M.-T., Han, B. W., Hsiao, C.-P., Zamore, P. D., Weng, Z., and Hung, J.-H. (2015). Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic Acids Res. Advance Access. doi: 10.1093/nar/gkv537

Contact

    Jui-Hung Hung <juihunghung `at` gmail.com>
    Chou Min-Te <poi5305 `at` gmail.com>
    Bo W Han <bowhan `at` me.com>